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Merge pull request #173 from csdms/mcflugen/stable-convert-remaining-…
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Convert remaining rst to myst on stable branch
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mcflugen authored Nov 21, 2024
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93 changes: 46 additions & 47 deletions CITATION.md
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If you use the Basic Model Interface for work/research
presented in a publication, we ask that you please cite:

```{eval-rst}
.. tab-set::
.. tab-item:: APA
Peckham, S.D., Hutton, E.W., and Norris, B., 2013. **A component-based
approach to integrated modeling in the geosciences: The design of CSDMS**.
*Computers & Geosciences*, 53, pp.3-12,
https://doi.org/10.1016/j.cageo.2012.04.002.
Hutton, E.W.H., Piper, M.D., and Tucker, G.E., 2020. **The Basic Model
Interface 2.0: A standard interface for coupling numerical models in the
geosciences**. *Journal of Open Source Software*, 5(51), 2317,
https://doi.org/10.21105/joss.02317.
.. tab-item:: BibTeX
.. code:: bibtex
@article{peckham2013component,
title={
A component-based approach to integrated modeling in the
geosciences: The design of CSDMS
},
author={Peckham, Scott D and Hutton, Eric WH and Norris, Boyana},
journal={Computers \& Geosciences},
volume={53},
pages={3--12},
year={2013},
publisher={Elsevier}
}
@article{hutton2020basic,
doi={10.21105/joss.02317},
url={https://doi.org/10.21105/joss.02317},
year={2020},
publisher={The Open Journal},
volume={5},
number={51},
pages={2317},
author={Eric W.H. Hutton and Mark D. Piper and Gregory E. Tucker},
title={
The Basic Model Interface 2.0: A standard interface for coupling
numerical models in the geosciences
},
journal={Journal of Open Source Software}
}
::::{tab-set}

:::{tab-item} APA
Peckham, S.D., Hutton, E.W., and Norris, B., 2013. **A component-based
approach to integrated modeling in the geosciences: The design of CSDMS**.
*Computers & Geosciences*, 53, pp.3-12,
https://doi.org/10.1016/j.cageo.2012.04.002.

Hutton, E.W.H., Piper, M.D., and Tucker, G.E., 2020. **The Basic Model
Interface 2.0: A standard interface for coupling numerical models in the
geosciences**. *Journal of Open Source Software*, 5(51), 2317,
https://doi.org/10.21105/joss.02317.
:::

:::{tab-item} BibTeX
```bibtex
@article{peckham2013component,
title={
A component-based approach to integrated modeling in the
geosciences: The design of CSDMS
},
author={Peckham, Scott D and Hutton, Eric WH and Norris, Boyana},
journal={Computers \& Geosciences},
volume={53},
pages={3--12},
year={2013},
publisher={Elsevier}
}
@article{hutton2020basic,
doi={10.21105/joss.02317},
url={https://doi.org/10.21105/joss.02317},
year={2020},
publisher={The Open Journal},
volume={5},
number={51},
pages={2317},
author={Eric W.H. Hutton and Mark D. Piper and Gregory E. Tucker},
title={
The Basic Model Interface 2.0: A standard interface for coupling
numerical models in the geosciences
},
journal={Journal of Open Source Software}
}
```
:::
::::
116 changes: 56 additions & 60 deletions docs/source/bmi.control_funcs.md
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Expand Up @@ -13,24 +13,23 @@ updating.

## *initialize*

```{eval-rst}
.. tab-set::
:sync-group: lang
::::{tab-set}
:sync-group: lang

.. tab-item:: SIDL
:sync: sidl
.. code-block:: java
int initialize(in string config_file);
.. tab-item:: Python
:sync: python
.. code-block:: python
:::{tab-item} SIDL
:sync: sidl
```java
int initialize(in string config_file);
```
:::

def initialize(self, config_file: str) -> None:
:::{tab-item} Python
:sync: python
```python
def initialize(self, config_file: str) -> None:
```
:::
::::

The `initialize` function accepts a string argument that gives the
path to its {term}`configuration file`.
Expand All @@ -57,24 +56,23 @@ formatted.

## *update*

```{eval-rst}
.. tab-set::
:sync-group: lang
::::{tab-set}
:sync-group: lang

.. tab-item:: SIDL
:sync: sidl
.. code-block:: java
int update();
.. tab-item:: Python
:sync: python
.. code-block:: python
:::{tab-item} SIDL
:sync: sidl
```java
int update();
```
:::

def update(self) -> None:
:::{tab-item} Python
:sync: python
```python
def update(self) -> None:
```
:::
::::

The `update` function advances the model by a single time step. This
is the model's own internal time step (as returned by the BMI
Expand All @@ -96,24 +94,23 @@ function can just return without doing anything.

## *update_until*

```{eval-rst}
.. tab-set::
:sync-group: lang
::::{tab-set}
:sync-group: lang

.. tab-item:: SIDL
:sync: sidl
.. code-block:: java
int update_until(in double time);
.. tab-item:: Python
:sync: python
.. code-block:: python
:::{tab-item} SIDL
:sync: sidl
```java
int update_until(in double time);
```
:::

def update_until(self, time: float) -> None:
:::{tab-item} Python
:sync: python
```python
def update_until(self, time: float) -> None:
```
:::
::::

The `update_until` function updates the model to a particular time,
as provided by its *time* argument.
Expand All @@ -134,24 +131,23 @@ to reflect that the model was updated to the requested time.

## *finalize*

```{eval-rst}
.. tab-set::
:sync-group: lang
::::{tab-set}
:sync-group: lang

.. tab-item:: SIDL
:sync: sidl
.. code-block:: java
int finalize();
.. tab-item:: Python
:sync: python
.. code-block:: python
:::{tab-item} SIDL
:sync: sidl
```java
int finalize();
```
:::

def finalize(self) -> None:
:::{tab-item} Python
:sync: python
```python
def finalize(self) -> None:
```
:::
::::

The `finalize` function should perform all tasks that take place
after exiting the model's time loop. This typically includes
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